The first law of computation (garbage in, garbage out) applies equally well to FBDD. These articles discuss the selection of compounds for fragment screening.
Blomberg et al, Design of compound libraries for fragment screening, J. Comput.-Aid. Mol. Des., 2009, 23, 513-525 DOI
Schuffenhauer et al, Library Design for Fragment Screening. Curr. Top. Med. Chem. 2005, 5, 751-762 link
Baurin et al, Design and Characterization of Libraries for Use in NMR Screening against Protein Targets. J. Chem Inf. Comp. Sci. 2004, 44, 2157-2166 DOI